Direct observation of gas molecules confined in the nanospace of porous materials by single-crystal X-ray diffraction (SXRD) technique is, significant because it leads to deep insight into the adsorption mechanism and the actual state of the adsorbents in molecular level. A recent study revealed that flexibility is one of the important factors to achieve periodic guest accommodation in the nanospace enabling direct observation of gas molecules. Here, we report a convenient strategy to tune the framework flexibility by just an atomic exchange in a ligand, which enables us to easily construct a soft nanospace as the best platform to study gas adsorption. Indeed, we succeeded to observe C2H2 and CO2 molecules confined in the pores of a flexible porous coordination polymer (PCP-N) in different configurations using SXRD measurement, whereas gas molecules in a rigid framework (PCP-C) isostructural to PCP-N were not seen crystallographically. The result of the coincident in situ powder X-ray diffraction and adsorption measurement for PCP-N unambiguously showed that the framework could flexibly transform to trap gas molecules with a commensurate fashion. In addition, for PCP-N, we found that the adsorbed gas molecules induced significant structural change involving dimensional change of the pore from one-dimensional to three-dimensional, and subsequently, additional gas molecules formed periodic molecular clusters in the nanospace.